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r493 ->HiC/UL/Trans

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chhylp123
2023-01-11 20:38:45 -05:00
parent a674110b23
commit 0613b18af9
19 changed files with 3230 additions and 461 deletions
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hic.cpp
+95 -9
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@@ -2142,6 +2142,7 @@ void print_hits_simp(ha_ug_index* idx, kvec_pe_hit* hits)
char dir[2] = {'+', '-'};
for (k = 0; k < hits->a.n; ++k)
{
if(((hits->a.a[k].s<<1)>>shif) == ((hits->a.a[k].e<<1)>>shif)) continue;
fprintf(stderr, "r-%lu-th\t%c\trs-utg%.6dl\t%lu\t%c\tre-utg%.6dl\t%lu\n",
hits->a.a[k].id,
dir[hits->a.a[k].s>>63], (int)((hits->a.a[k].s<<1)>>shif)+1, hits->a.a[k].s&idx->pos_mode,
@@ -7088,7 +7089,7 @@ void get_bub_graph(ma_ug_t* ug, bubble_type* bub)
adjecent = 0;
while (pre_id != v)
{
if(connect_bub_occ(bub, pre_id>>1, bub->check_het) > 0)
if(connect_bub_occ(bub, pre_id>>1, bub->check_het) > 0)///some bubbles between v and k
{
adjecent = 1;
break;
@@ -16480,7 +16481,7 @@ void optimize_u_trans(kv_u_trans_t *ovlp, kvec_pe_hit* hits, ha_ug_index* idx)
for (i = 0; i < ovlp->n; i++){
x = &(ovlp->a[i]);
if(x->qn > x->tn) continue;
if(x->f != RC_2 || x->del) continue;
if(x->f != RC_2 || x->del) continue;///no need to adjust RC_0/RC_1
occ = get_oe_occ(x->qn, x->tn, hits, idx) + get_oe_occ(x->tn, x->qn, hits, idx);///how many UL bridging qn and tn
kv_pushp(u_trans_t, k_trans, &p);
(*p) = (*x); p->nw = (x->nw*(1-(((double)(occ<<1))/((double)(hits->occ.a[x->qn]+hits->occ.a[x->tn])))));
@@ -16731,8 +16732,13 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_o
write_hc_hits(&sl.hits, idx->ug, asm_opt.output_file_name);
}
sl.hits.uID_bits = idx->uID_bits; sl.hits.pos_mode = idx->pos_mode;
optimize_u_trans(&(idx->t_ch->k_trans), &sl.hits, idx);
filter_kv_u_trans_t(&(idx->t_ch->k_trans), idx->ug, 0.5);
/***debug***/
if(sl.hits.idx.n == 0) idx_hc_links(&(sl.hits), idx, NULL);
// optimize_u_trans(&(idx->t_ch->k_trans), &sl.hits, idx);
// filter_kv_u_trans_t(&(idx->t_ch->k_trans), idx->ug, 0.5);
/***debug***/
// print_kv_u_trans_t(&(idx->t_ch->k_trans), idx->ug);
// flter_by_cov(idx, &sl.hits, 2);
// update_hits(idx, &sl.hits, idx->t_ch->is_r_het);
@@ -16782,13 +16788,15 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_o
/*******************************for debug************************************/
mc_solve(NULL, NULL, &k_trans, idx->ug, idx->read_g, 0.8, R_INF.trio_flag,
(bub.round_id == 0? 1 : 0), s->s, 1, &bub,
&(idx->t_ch->k_trans), 0, 0/**(((bub.round_id+1) == bub.n_round)?1:0)**/);
&(idx->t_ch->k_trans), 0, /**(((bub.round_id+1) == bub.n_round)?1:0)**/0);
// mc_solve(NULL, NULL, &k_trans, idx->ug, idx->read_g, 0.8, R_INF.trio_flag,
// (bub.round_id == 0? 1 : 0), s->s, 1, NULL, &(idx->t_ch->k_trans), 0, 0);
// if((bub.round_id+1) == bub.n_round) {
// prt_debug_hic(asm_opt.output_file_name, idx->ug, idx, opt, &sl.hits,
// &(idx->t_ch->k_trans), &k_trans, &link, s->s, &(bub));
// }
/**
if((bub.round_id+1) == bub.n_round) {
prt_debug_hic(asm_opt.output_file_name, idx->ug, idx, opt, &sl.hits,
&(idx->t_ch->k_trans), &k_trans, &link, s->s, &(bub));
}
**/
/*******************************for debug************************************/
label_unitigs_sm(s->s, NULL, idx->ug);
@@ -16853,6 +16861,84 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_o
return 1;
}
void bp_solve(ug_opt_t *opt, kv_u_trans_t *ref, ma_ug_t *ug, asg_t *sg, bubble_type *bub, double cis_rate)
{
uint64_t k, i, v, nvx, n[3], nv; u_trans_t *z;
kv_u_trans_t in; memset(&in, 0, sizeof(in));
ma_utg_t *u = NULL; asg_arc_t *av; double w;
ps_t *s = init_ps_t(11, ug->g->n_seq);
for (i = 0; i < ug->g->n_seq; i++) {
s->s[i] = 0;
if((ug->g->seq[i].del) || (IF_HOM(i, (*bub)))) {
continue;
}
u = &ug->u.a[i];
if(u->m == 0 || u->n == 0) continue;
for (k = n[0] = n[1] = n[2] = 0; k < u->n; k++) {
if(R_INF.trio_flag[u->a[k]>>33] == FATHER) n[1]++;
else if(R_INF.trio_flag[u->a[k]>>33] == MOTHER) n[2]++;
else n[0]++;
}
if(n[1] >= n[2] && n[1] >= n[0]) s->s[i] = 1;
else if(n[2] >= n[1] && n[2] >= n[0]) s->s[i] = -1;
}
kv_resize(u_trans_t, in, ref->n);
for (k = in.n = 0; k < ref->n; k++) {
if((IF_HOM(ref->a[k].qn, (*bub))) || (IF_HOM(ref->a[k].tn, (*bub))) || ref->a[k].del) {
continue;
}
kv_push(u_trans_t, in, ref->a[k]);
}
if(cis_rate > 0) {
nvx = ug->g->n_seq<<1;
for (v = 0; v < nvx; v++) {
if((ug->g->seq[v>>1].del) || (IF_HOM((v>>1), (*bub)))) continue;
av = asg_arc_a(ug->g, v); nv = asg_arc_n(ug->g, v);
for (i = 0; i < nv; i++) {
if((av[i].del) || (av[i].v>>1) == (v>>1) ||
(ug->g->seq[av[i].v>>1].del) || (IF_HOM((av[i].v>>1), (*bub)))) {
continue;
}
w = ((double)av[i].ol)*cis_rate;
if(w <= 0) continue;
kv_pushp(u_trans_t, in, &z);
memset(z, 0, sizeof((*z)));
z->f = RC_3; z->nw =-w; z->rev = (v^av[i].v)&1;
z->qn = v>>1; z->tn = av[i].v>>1;
z->qs = 0; z->qe = sg->seq[z->qn].len;
if(av[i].ol < sg->seq[z->qn].len) {
if(v&1) {
z->qe = z->qs + av[i].ol;
} else {
z->qs = z->qe - av[i].ol;
}
}
z->ts = 0; z->te = sg->seq[z->tn].len;
if(av[i].ol < sg->seq[z->tn].len) {
if(av[i].v&1) {
z->ts = z->te - av[i].ol;
} else {
z->te = z->ts + av[i].ol;
}
}
}
}
}
// fprintf(stderr, "[M::%s::] ==> nup::%lu\n", __func__, nup);
clean_u_trans_t_idx_adv(&in, ug, sg);
mc_solve(NULL, NULL, &in, ug, sg, 0.8, NULL, 0, s->s, 1, bub, ref, 0, 0);
label_unitigs_sm(s->s, NULL, ug);
destory_ps_t(&s); kv_destroy(in); kv_destroy(in.idx);
}
spg_t *hic_short_pre_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_opt_t *opt, kvec_pe_hit **rhits)
{
// double index_time = yak_realtime();